Identification and Characterization of MicroRNAs and Their Targets That Respond to Powdery Mildew in Melon

Abstract

To identify microRNAs (miRNAs) responsive to powdery mildew (PM) infection and elucidate their regulatory roles in melon PM resistance, thereby laying a foundation for deciphering the underlying molecular mechanisms, we combined high-throughput sequencing with bioinformatics analysis to screen PM-responsive miRNAs and their target genes using PM-resistant and PM-susceptible melon genotypes. In total, 113 non-redundant miRNAs were identified in both genotypes, including 70 known and 43 novel miRNAs. Subsequent differential expression analysis revealed distinct miRNA responses to PM infection between resistant and susceptible genotypes. Upon PM inoculation, 13 miRNAs showed significant differential expression in both susceptible and resistant genotypes. In addition, four miRNAs, including miR164c, miR396a, miR398a and miRn39, displayed differential expression specifically in the susceptible genotype. Conversely, five miRNAs (miR167c, miR398b, miR399g, miR530a and miRn8) showed differential expression exclusively in the resistant genotype upon PM infection. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses demonstrated that these miRNAs mediate melon’s susceptibility or resistance to PM by modulating plant immune homeostasis, antioxidant metabolism, and pathogen-triggered cell death. Quantitative real-time PCR (qRT-PCR) validation confirmed a negative regulatory relationship between the expression of PM-responsive miRNAs and their predicted target genes. Collectively, our findings provide novel insights and candidate targets for further investigations into miRNA functions and regulatory mechanisms underlying melon PM resistance.